Molecular characterisation and pathogenicity of <Emphasis Type="Italic">Aspergillus</Emphasis> Sect. <Emphasis Type="Italic">Nigri</Emphasis> causing Aspergillus vine canker of table grapes in Italy

Thirty-two isolates belonging to black aspergilli (Aspergillus section Nigri) associated to vine canker disease of grapevine were collected in seven vineyards located in southeastern Sicily (Italy). Molecular analysis was performed to identify the isolates by multilocus sequence analysis. Amplification of part of the β-tubulin gene (benA) and partial calmodulin (CaM) gene were performed using the Bt2a, Bt2b and CL1, CL2A primers, respectively. Molecular characterisation showed a high distribution of Aspergillus niger “aggregate” species on grapes in Sicily and in particular of A. niger (21 isolates), A. tubingensis (9 isolates), and A. carbonarius (2 isolates). The 21 isolates of A. niger found to belong within the newly described cryptic species A. awamori. Six isolates (3 of A. tubingensis, 2 of A. carbonarius, and 1 of A. niger) were used in pathogenicity studies on mature canes of cv. Italia grape. All species caused Aspergillus vine canker equally well, with no differences in virulence.     

Ochratoxin a in Grapes and Wine

The mycotoxin ochratoxin A is a potent nephrotoxin and a possible human carcinogen. It occurs in a variety of plant products, including wine, grape juice and dried vine fruits. Several surveys have shown that the range of ochratoxin A contents detected in wine produced in Europe varied between 0.01 and 3.4gl^–1. Both incidence and concentration of the toxin were higher in wines from southern regions and increased in the order white < rosè < red. In Italy, field trials were conducted in 1999 and 2000 to study fungi associated with grapes and their ability to produce ochratoxin. Aspergillus and/or Penicillium strains were present on grapes, starting from setting in a few vineyards. The highest level of grape colonisation was found at early veraison in 1999 and at ripening in 2000. In both years, 95% of strains belonged to the genus Aspergillus. Aspergillus niger aggregate was dominant, with about 50% of the ochratoxin-positive strains identified as A carbonarius. Other authors have confirmed the relevance of these fungi and underlined the contribution of A. carbonarius to the ochratoxin contamination of wine. This species is very invasive and colonises and penetrates berries, even without skin damage. It emerges that temperature, rain and relative humidity are the main factors that influence ochratoxin production in grapes.     

云南葡萄产区葡萄炭疽病病原鉴定及致病力分析

为了明确引起云南葡萄产区炭疽病的病原种类,利用形态鉴定和特异性引物分子检测相结合的方法对从云南省主要葡萄产区采集的60株炭疽病菌菌株进行了鉴定。葡萄炭疽病菌菌株的菌落形态和生长速率与对照菌株尖孢炭疽菌Colletotrichum acutatum差异不明显,但其分生孢子大小显著小于尖孢炭疽菌,附着胞深褐色,球形或不规则形。胶孢炭疽菌Colletotrichum gloeosporioides特异性引物CgInt/ITS4从供试葡萄炭疽病菌菌株基因组DNA中扩增出1条约500 bp的特异性条带,而尖孢炭疽菌特异性引物CaInt2/ITS4对葡萄炭疽病菌无扩增条带。研究表明,引起云南葡萄主产区炭疽病的病原为胶孢炭疽菌;供试胶孢炭疽菌对红提葡萄均有致病力,但菌株致病力差异较大,对番茄和草莓存在交叉侵染的能力,且对多菌灵的敏感性较尖孢炭疽菌高。     

A Species-Specific PCR Assay Based on the Calmodulin Partial Gene for Identification of Fusarium Verticillioides, F. Proliferatum and F. Subglutinans

Fusarium proliferatum, F. subglutinans and F. verticillioides are the most important Fusarium species occurring on maize world-wide, capable of producing a wide range of mycotoxins which are a potential health hazard for animals and humans. The ribosomal internal transcribed spacer and a portion of the calmodulin gene were sequenced and analysed in order to design species-specific primers useful for diagnosis. The primer pairs were based on a partial calmodulin gene sequence. Three pairs of primers (PRO1/2, SUB1/2 and VER 1/2) produced PCR products of 585, 631 and 578bp for F. proliferatum, F. subglutinans and F. verticillioides, respectively. Primer specificity was confirmed by analyzing DNA of 150 strains of these species, mostly isolated from maize in Europe and USA. The sensitivity of primers was 12.5 pg when the pure total genomic DNA of each species was analyzed. The developed PCR assay should provide a powerful tool for the detection of toxigenic fungi in maize kernels.     

Molecular Diversity of Agriculturally Important Aspergillus Species

Although Aspergillus species are not usually considered as serious plant pathogens, Aspergilli are frequently encountered in plant products. The most important consequence of their presence is mycotoxin contamination. The main mycotoxins produced by Aspergilli are the aflatoxins, ochratoxin A and patulin, which are produced by a variety of Aspergillus species in different plant commodities. Phylogenetic analysis of sequences of the ribosomal RNA gene cluster is useful for clarifying taxonomic relationships among toxigenic Aspergilli causing pre- and postharvest contamination of agricultural products. Molecular data has enabled us to clarify the taxonomy of black Aspergilli, A. flavus and its relatives, and sections Circumdati and Clavati, which include ochratoxin and patulin-producing species. Phylogenetically unrelated species were found to produce the same mycotoxins, indicating that mycotoxin-producing abilities of the isolates have been lost (or gained) several times during the evolution of the genus. The data also indicate that biosynthetic gene-based probes are necessary for molecular detection of these mycotoxin-producing organisms. The organisation of the biosynthetic genes of patulin and ochratoxins is unknown, although experiments are in progress in several laboratories to clarify the genetic background of biosynthesis of these mycotoxins. Identification of biosynthetic genes responsible for mycotoxin production is essential for clarifying the evolution of mycotoxin biosynthesis in Aspergilli, and to develop specific gene probes for the detection of mycotoxin-producing Aspergilli in agricultural products.     

Ochratoxin A-producing fungi in Spanish wine grapes and their relationship with meteorological conditions

Forty vineyards from four wine making regions of Spain were sampled at three different growth stages in 2002 and 2003. The aim was to study the fungi associated with grapes and their ability to produce ochratoxin A (OTA) on synthetic media. Among the total mycoflora, 464 (7.7%) and 648 (10.8%) Aspergillus section Nigri (black aspergilli) strains were isolated in 2002 and 2003, respectively, and were classified into three groups: isolates with uniseriate heads, A. niger aggregate and A. carbonarius. The latter presented the highest percentage of OTA-positive strains (82% in 2002 and 76% in 2003) and produced the highest levels of toxin (2.5–25 μg g⁻¹). The sampling year, sampling date, the region and their interactions presented significant differences in the number of black aspergilli isolated. Most black aspergilli were found in 2003 and at harvest. A positive correlation between the number of black aspergilli found in grapes and the temperature in the field was found. Grapes from 2003, the warmest year, and from Costers del Segre, the warmest region, were significantly the most contaminated. No significant correlation between black aspergilli presence and other meteorological factors such as relative humidity or rainfall could be established. Musts from all the vineyards were also analysed in both years, although no OTA was found in either year.     

Phylogeny and Molecular Diagnosis of Mycotoxigenic Fungi

Phylogenetic studies of the fungi that produce the five major groups of mycotoxins are reviewed, with a focus on studies employing ribosomal and/or β-tubulin (BenA) gene sequences. The toxins aflatoxin and ochratoxin A are produced by several Aspergillus and Penicillium species classified in the Trichocomaceae, Eurotiales. The toxins fumonisin, deoxynivalenol and zearalenone are produced by several Fusarium species classified in the Nectriaceae, Hypocreales. Studies of ribosomal genes have revealed that the present generic concepts for Aspergillus, Penicillium and Fusarium will require some adjustment in order to conform to phylogenetic principles. Phylogenetic studies have resulted in generally narrower species concepts in all three genera but there is good correlation between these species and mycotoxin production. The development of molecular diagnostics for the critical mycotoxigenic species is considered, with particular emphasis on the development of DNA hybridization probes that can be used to detect and identify multiple species using species and/or clade specific oligonucleotides designed from one or more genes. As an illustration, a virtual array for identifying Aspergillus species and groups of species producing aflatoxin is presented, based on oligonucleotides selected and optimized from a database of internal transcribed spacer and partial β-tubulin sequences assembled from GenBank. It was possible to design acceptable oligos for all species and groups in the complex using the β-tubulin gene, but only for one species and the larger group using the less variable internal transcribed spacer of the ribosomal DNA.     

Incidence and diversity of the fungal genera Aspergillus and Penicillium in Portuguese almonds and chestnuts

Almonds (Prunus dulcis (Miller) D.A. Webb) and European (sweet) chestnuts (Castanea sativa Miller) are of great economic and social impact in Mediterranean countries, and in some areas they constitute the main income of rural populations. Despite all efforts to control fungal contamination, toxigenic fungi are ubiquitous in nature and occur regularly in worldwide food supplies, and these nuts are no exception. This work aimed to provide knowledge on the general mycobiota of Portuguese almonds and chestnuts, and its evolution from field to the end of storage. For this matter, 45 field chestnut samples and 36 almond samples (30 field samples and six storage samples) were collected in Trás-os-Montes, Portugal. All fungi belonging to genus Aspergillus were isolated and identified to the section level. Fungi representative of other genera were identified to the genus level. In the field, chestnuts were mainly contaminated with the genera Fusarium, Cladosporium, Alternaria and Penicillium, and the genus Aspergillus was only rarely found, whereas almonds were more contaminated with Aspergillus. In almonds, Aspergillus incidence increased significantly from field to the end of storage, but diversity decreased, with potentially toxigenic isolates belonging to sections Flavi and Nigri becoming more significant and widespread throughout storage. These fungi were determined to be moderately associated, which can be indicative of mycotoxin co-contamination problems if adequate storage conditions are not secured.     

雪松疫霉(Phytophthora lateralis)的快速分子检测

由雪松疫霉(Phytophthora lateralis)引起的疫病是一类植物检疫性病害。为建立该病原菌的快速检测技术,本文比较分析了雪松疫霉和其他疫霉的tRNA序列,在此基础上设计了一对检测雪松疫霉的特异性引物T1/T2,该对引物从雪松疫霉中扩增得到1条192 bp的条带,而其他15种疫霉和其他真菌菌株均无扩增条带,表明该对引物对雪松疫霉具有特异性。在25μL PCR反应体系中,引物T1/T2检测灵敏度为10 pg基因组DNA;而以引物T3/T4和T1/T2进行巢式PCR扩增,能够检测到1 fg基因组DNA,使检测灵敏度提高了10 000倍。该检测体系对灭菌水中游动孢子的检测灵敏度可达0.5个游动孢子,对人工接种发病的植物组织能够特异性地检测到该病原菌。此外,进一步建立了该病原菌的实时荧光定量PCR检测体系。     

Improved PCR for identification of members of the genus Xanthomonas

A PCR-based system was developed to reliably and robustly identify group I and II members of the genus Xanthomonas. Primer sets developed from three gene targets namely fyuA, ITS and gumD were evaluated in the study. Primer sets were evaluated using DNA extracted from 45 Xanthomonas strains representing 25 species broadly covering the genus. Fifteen non-Xanthomonas strains of plant-associated bacteria including phylogenetically closely related species Stenotrophomonas maltophilia and Xylella fastidiosa were also tested. The primers targeting fyuA amplified DNA from all xanthomonads except X. theicola, while the ITS primers amplified a DNA fragment of 254 bp in all 45 Xanthomonas strains; whereas no amplification was observed for non-xanthomonads. The gumD primers allowed efficient amplification of DNA in 38 out of 39 isolates from Group II, whereas no or very weak amplification occurred with DNA from Group I members. Internal controls of primers targeting bacterial 16S rDNA or plant 26S mitochondrial rDNA were successfully applied in multiplex PCRs for testing bacterial cultures or plant tissue, respectively. The findings give us a PCR based approach that can reliably and effectively differentiate xanthomonads from non-xanthomonads as well as separating the strains belonging to the two described groups of the genus Xanthomonas. The study thus offers valuable tools for disease surveillance and management. It can effectively be applied in rapid assessment of new disease occurrences, for which no specific detection tools could be in place.     

Specific primers for Xanthomonas vesicatoria, a tomato bacterial spot causal agent

Xanthomonas vesicatoria is a member of the species complex associated with tomato bacterial spot. New and specific primers for X. vesicatoria were developed and validated. The primers were highly specific and detection was positive using purified bacterial DNA, bacterial suspensions and foliar lesions. These primers represent an additional tool for detection and identification of one of the species involved in this important disease complex.     

建兰胶孢炭疽菌ITS序列分析及其PCR快速检测

由胶孢炭疽菌Colletotrichum gloeosporioides引起的炭疽病是建兰的重要病害.为建立快速检测该病原菌的方法,以ITSl/ITS4为引物,对15个建兰胶孢炭疽菌的ITS进行PCR扩增及测序,将测定的序列与炭疽菌属其它种的ITS序列进行比对分析,设计特异性引物CFl/CR1,并通过常规和巢式PCR对建兰胶孢炭疽菌进行检测.结果显示,15个菌株中有13个菌株ITS序列与该菌的模式种序列相似性高达99％以上,而另外2个菌株相似性则为86％;供试菌株在系统发育树上聚为2个不同的分支;引物CFl/CR1通过常规PCR可从1 ng的建兰胶孢炭疽菌基因组DNA中扩增到目的条带,而利用引物ITSl/ITS4和CF1/CR1通过巢式PCR可从1 pg的基因组DNA中扩增到目的条带,即巢式PCR反应检测灵敏度较常规PCR至少高1 000倍.表明建立的巢式PCR法可从自然感病的建兰叶片组织中检测到胶孢炭疽菌.     

Stilbene oligomer phytoalexins in grape as a response to Aspergillus carbonarius infection

Stilbenes are grapevine phytoalexins elicited by biotic and abiotic agents; Aspergillus carbonarius is a widespread ochratoxin A producing fungus present in warm conditions, such as in Southern Italy. To increase the knowledge on biosynthesis of stilbene oligomers induced by A. carbonarius infection, grape berries of the Southern Italian grape cv. Negro Amaro were inoculated. Significant increase of trans-resveratrol and resveratrol dimers and oligomers, such as caraphenol, E-ε-viniferin, ω-viniferin, δ-viniferin, α-viniferin, E-miyabenol C, and two tetramers, was observed, and concomitant decrease of glycoside derivatives. These findings improve the knowledge on the phytoalexin production as response against this pathogen.     

Differentiation of the closely related species,Alternaria solani and A. tomatophila,by molecular and morphological features and aggressiveness

The main causal agent of early blight, the noxious disease of solanaceous crops, is generally considered to be Alternaria solani Sorauer (in a broad sense). However, heterogeneity in many morphological features of this pathogen has been noted suggesting that the disease may not be caused by a single species. Recent research has revealed that several large-spored Alternaria species may cause disease of potato and tomato including A. solani sensu stricto and A. tomatophila. The goal of our research was to compare Russian large-spored Alternaria isolates from tomato and potato to test the hypothesis that early blight of tomato and potato are caused by different species. Cluster analysis of genetic distances estimated from 12 polymorphic molecular markers (universally primed-polymerase chain reaction and randomly amplified polymorphic DNA) revealed two groups of isolates accepted here as A. solani and A. tomatophila that were supported by morphology and host plant association. Differentiation of species was supported by phylogeny derived from the DNA sequences of a portion of the Alt a1, gpd and calmodulin genes. Species-specific primers based on the Alt a1 and calmodulin gene sequences for both species were designed. Under laboratory conditions, A. solani isolates were equally aggressive on both tomato and potato, whereas A. tomatophila was highly aggressive to tomato but only weakly aggressive to potato. In the field, A. solani was isolated from potato, tomato and from several wild potato species including S. schickii, S. papita and S. kurtzianum. The majority (90 %) of A. solani isolates carried the mating type locus 1 (MAT1) idiomorph MAT1-1 while the majority (88 %) of A. tomatophila isolates carried the MAT1-2 idiomorph.     

Species-specific DNA markers for identification of two root-knot nematodes of coffee: Meloidogyne arabicida and M. izalcoensis

Seven root-knot nematodes (RKN), including Meloidogyne exigua, M. incognita, M. paranaensis, M. enterolobii, M. arabicida, M. izalcoensis and M. arenaria are major pathogens of coffee crop in the Americas. Species-specific primers for their identification have been developed for five of them and constitute a fast and reliable method of identification. Here we report a PCR-based assay for specific detection of M. arabicida and M. izalcoensis. Random Amplified Polymorphic DNA fragments specific for these two species were converted into sequence characterized amplified region (SCAR) markers. PCR amplification using the SCAR primers produced a specific fragment of 300 bp and 670 bp for M. arabicida and M. izalcoensis, respectively, which were absent in other coffee-associated Meloidogyne spp. tested. SCAR primers also allowed successful amplification of DNA from single second-stage juveniles (J2), males and females. In addition, these primers were able to unambiguously detect the target species in nematode suspensions extracted from soil and roots samples, in different isolates of the same species or when used in multiplex PCR reactions containing mixtures of species. These results demonstrated the effectiveness of these SCAR markers and their multiplex use with those previously developed for M. exigua, M. incognita, M. paranaensis, M. enterolobii and M. arenaria constitute an essential detection tool. This diagnostic kit will contribute for specific J2 identification of the major RKN infecting coffee from field samples in the Americas.     

Development of two species-specific primer sets to detect the cereal cyst nematodes Heterodera avenae and Heterodera filipjevi

Twelve Heterodera species are of major economic significance in wheat and barley. Of these, H. avenae, H. filipjevi and H. latipons are among the most important ones, and sometimes coexist. The identification of Heterodera species using morphological characteristics is time consuming, requires specialized skill and can be imprecise, especially when they occur mixed in field populations. Molecular techniques can provide a more accurate way for nematode identification. This study reports the results of experiments targeting the mitochondrial cytochrome oxidase subunit 1 (COI) gene to develop species-specific primers that could be used for the identification of H. avenae and H. filipjevi. The COI gene of 9 Heterodera spp. and Punctodera punctata was partially sequenced and the resultant sequences were aligned to find unique sites suitable for the design of primers. The alignment showed variability between H. avenae, H. filipjevi and other Heterodera species. Two sets of species-specific primers were identified for the identification of both species and the conditions for their use in PCR were optimised. The specificity of the designed primers was checked by comparison with one population of P. punctata and populations of 14 other Heterodera species, nine populations of H. avenae and 10 populations of H. filipjevi originating from different countries. To test the sensitivity, the PCR was run with DNA extracted from five second-stage juveniles (J2) of H. avenae or five J2 of H. filipjevi mixed with DNA extracted from varying numbers of J2 of H. latipons. It was possible to detect as few as five J2 of H. avenae or H. filipjevi among 100 J2 of H. latipons. The two primers sets allow the detection of H. avenae and H. filipjevi where they occur in mixed populations with other Heterodera spp.     

Detection of botryosphaeriaceous species in environmental samples using a multi‐species primer pair

Botryosphaeriaceous species are significant grapevine trunk pathogens worldwide, which can be difficult to identify to species level using conventional morphological methods. This study developed and optimized a quick, reliable molecular identification method that could facilitate investigations into the epidemiology of these diseases in vineyards. The multi‐species primers, BOT100F and BOT472R, amplified a 371–372 bp portion of the rRNA gene region from the six botryosphaeriaceous species commonly found in New Zealand vineyards. In silico analysis indicated that they would amplify DNA from six of the 12 lineages of the Botryosphaeriaceae, including all of the main species pathogenic to grapevines. A detection sensitivity of 1 and 0·1 pg DNA in standard and nested PCR, respectively, was achieved and this was calculated as equivalent to 2·5 conidia. Validation of the primers for environmental samples showed that their specificity was not compromized by the presence of competing DNA templates extracted from wood and soil. Single stranded conformational polymorphism (SSCP) analysis of the amplicons could resolve Neofusicoccum australe, N. luteum, Diplodia mutila and D. seriata, but did not differentiate between N. parvum and N. ribis. The optimized PCR‐SSCP was used to identify botryosphaeriaceous species present in rainwater traps collected over 1 year in a vineyard known to contain infected vines. It could detect multiple species in individual samples and demonstrated differences in the dispersal patterns of conidia from different species. Given the specificity and sensitivity of this method it could prove useful in epidemiology studies involving the numerous botryosphaeriaceous species that infect a wide range of host species.     

A nested multiplex PCR for species-specific identification and detection of Botryosphaeriaceae species on mango

Lasiodiplodia theobromae (Pat.) Griff. & Maubl, Neofusicoccum parvum Pennycook & Samuels, N. mangiferae Syd. & P. Syd., and Fusicoccum aesculi Corda, all anamorphs of Botryosphaeriaceae species, are the causal agents of mango stem-end rot and fruit rot in Taiwan. Identification of these fungal species based on morphology has not been easy due to their extensive plasticity for some of the morphological characters. To aid reliable identification of Botryosphaeriaceae species associated with mango fruits, four pairs of species-specific primers were designed according to sequences of the ribosomal internal transcribed spacers (ITS), and a rapid method was established based on nested multiplex polymerase chain reaction (PCR) in this study. To perform the analysis, PCR was first run with ITS1 and ITS4 as the primers, followed by a second PCR with the addition of all four sets of species-specific primers. With this method, a low limit of 100?fg^-1?pg of purified fungal DNA was detectable. It could also successfully detect L. theobromae, N. parvum, N. mangiferae and F. aesculi in total DNA extracted from inoculated mango fruits. This assay provides a rapid and sensitive method for the identification of Botryosphaeriaceae species and diagnosis of mango fruit rot and stem-end rot as well.     

Developing Groundnut Lines with Resistance to Seed Colonisation by Toxin-producing Strains of Aspergillus Species

Abstract

Evidence for the possible development of groundnut (Arachis hypogaea L.) cultivars with favourable agronomic characteristics and resistance to aflatoxinproducing strains of Aspergillus species is presented. In studies of F₂ and F₃ progenies from crosses of resistant and susceptible genotypes data on the frequency distribution and least square estimates of genetic effects showed the possibility of selecting for resistance to seed colonisation by the fungus. Yield, value and seed quality data for seven advanced lines developed by using pedigree selection from crosses showed that potential favourable groundnut cultivars may be developed.